Dear mixOmics team,
I have been using mixOmics package for my research and have recently started working with longitudinal samples, where I have 2 time points sampling on repeated individuals distributed in 2 groups of indiviuals.
I am working with metabolomic datas. Due to the large amount of metabolites and oa small number of individuals (non-balanced), I am well awared of the potential biais in the models I am using.
To examine how individuals are displayed in regards to groups and time, using all metabolites, in an unsupervised way, I need to perform a PCA.
However, in order to focus on the effect of treatment on my groups and reduce invididual variation, I am using a multilevel PCA, where I have used the individual number as a multilevel agrument.
I am having difficulty interpreting the results and would appreciate your expert advice.
-When I performed a PCA without a multilevel argument, the groups seemed to overlap, with one group showing changes after treatment.
-However, when I used a PCA with multilevel argument the four groups were distinguished and there was a greated separation for the red goup. The blue group, which showed less obvious changes in the PCA without the multilevel argument, showed changes in the multilevel PCA. However the multilevel PCA suggests that metabolome of the groups were different at baseline and that the difference between the two groups at baseline and after treatment is conserved.
My concern is that I am introducing some form of supervision of my groups by using the multilevel argument as I did. Shoult I trust my model and interpret the multilevel PCA? Or is there a better way to analyze my data to visualize is the metabolome is modified after treatment, and in a different way dependinf on the treatment ?
I apologize for the level of my explanation, and thank you in advance for any input you can provide on this,
Best regards,
Maëlle.